Photodynamic therapy (PDT) is a method for inactivating cells (viral, bacterial and cancer cells) using photosensitizers (PS) and light of various wavelengths. Helicobacter pylori might be easily affected by light because it has few genes to repair light-induced DNA damage. In vitro PDT against H. pylori was conducted using endoscopic white light and methylene blue (MB) as the PS before application to in vivo study. The bactericidal effects were measured by counting viable cells after PDT. The degree of oxidative damage of DNA was confirmed using alkaline gel electrophoresis, real-time PCR (RT-PCR) and an assay of 8-hydroxy-2-deoxyguanosine (8-OHdG). In the control group, the number of viable cells was maintained constantly during the experiment. In the groups treated with either 0.2 mg/ml MB alone or white light with 0.02 mg/ml MB for 10 min, bacteria decreased approximately a hundredfold. The killing effect increased proportionally to the PS concentration and the duration of irradiation. DNA damage by PDT proven by alkaline gel electrophoresis, RT-PCR and assay of 8-OHdG, was greater in PDT-treated groups than in control. PDT using MB and endoscopic white light showed effective bactericidal activity in vitro by oxidative DNA damage of H. pylori.